GSAgm-package: GSAgm package

Description

This package runs gene set analyses on SNP and RNA data. See individual functions for details.

Arguments

Details

Package:

GSAgm

Type:

Package

Version:

1.0

Date:

2013-12-04

License:

GPL-2

References

1. Biernacka JM, Jenkins GD, Wang L, et al. Use of the gamma method for self-contained gene-set analysis of SNP data. Eur J Hum Genet 2012;20(5):565-71. 2. Fridley BL, Jenkins GD, Grill DE, et al. Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study. Sci Rep 2013;3:2898.

3. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26(1):139-40.

4. Zaykin DV, Zhivotovsky LA, Czika W, et al. Combining p-values in large-scale genomics experiments. Pharm Stat 2007;6(3):217-26.

5. Fridley, B.L., and Biernacka, J.M. (2011). Gene set analysis of SNP data: benefits, challenges, and future directions. Eur J Hum Genet 19, 837-843.